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https://www.readbyqxmd.com/read/28337390/an-rbcl-reference-library-to-aid-in-the-identification-of-plant-species-mixtures-by-dna-metabarcoding
#1
Karen L Bell, Virginia M Loeffler, Berry J Brosi
PREMISE OF THE STUDY: DNA metabarcoding has broad-ranging applications in ecology, aerobiology, biosecurity, and forensics. A bioinformatics pipeline has recently been published for identification using a comprehensive database of ITS2, one of the common plant DNA barcoding markers. There is, however, no corresponding database for rbcL, the other primary marker used in plants. METHODS: Using publicly available data, we compiled a reference library of rbcL sequences and trained databases for use with UTAX and RDP classifier algorithms...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28327596/genetic-polymorphisms-of-54-mitochondrial-dna-snp-loci-in-chinese-xibe-ethnic-minority-group
#2
Chun-Mei Shen, Li Hu, Chun-Hua Yang, Cai-Yong Yin, Zhi-Dan Li, Hao-Tian Meng, Yu-Xin Guo, Ting Mei, Feng Chen, Bo-Feng Zhu
We analyzed the genetic polymorphisms of 54 mitochondrial DNA (mtDNA) variants in Chinese Xibe ethnic minority group. A total of 137 unrelated healthy volunteers from Chinese Xibe group were the objects of our study. Among the selected loci, there were 51 variable positions including transitions and transversions, and single nucleotide transitions were common (83.93%) versus transversions. These variations defined 64 different mtDNA haplotypes exclusive of (CA)n and 9 bp deletion variation. The haplotype diversity and discrimination power in Xibe population were 0...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325121/dna-extraction-and-barcode-identification-of-development-stages-of-forensically-important-flies-in-the-czech-republic
#3
Tereza Olekšáková, Martina Žurovcová, Vanda Klimešová, Miroslav Barták, Hana Šuláková
Several methods of DNA extraction, coupled with 'DNA barcoding' species identification, were compared using specimens from early developmental stages of forensically important flies from the Calliphoridae and Sarcophagidae families. DNA was extracted at three immature stages - eggs, the first instar larvae, and empty pupal cases (puparia) - using four different extraction methods, namely, one simple 'homemade' extraction buffer protocol and three commercial kits. The extraction conditions, including the amount of proteinase K and incubation times, were optimized...
March 21, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28324847/species-identification-in-forensic-samples-using-the-spindel-approach-a-ghep-isfg-inter-laboratory-collaborative-exercise
#4
Cíntia Alves, Rui Pereira, Lourdes Prieto, Mercedes Aler, Cesar R L Amaral, Cristina Arévalo, Gabriela Berardi, Florencia Di Rocco, Mariela Caputo, Cristian Hernandez Carmona, Laura Catelli, Heloísa Afonso Costa, Pavla Coufalova, Sandra Furfuro, Óscar García, Anibal Gaviria, Ana Goios, Juan José Builes Gómez, Alexis Hernández, Eva Del Carmen Betancor Hernández, Luís Miranda, David Parra, Susana Pedrosa, Maria João Anjos Porto, Maria de Lurdes Rebelo, Matteo Spirito, María Del Carmen Villalobos Torres, António Amorim, Filipe Pereira
DNA is a powerful tool available for forensic investigations requiring identification of species. However, it is necessary to develop and validate methods able to produce results in degraded and or low quality DNA samples with the high standards obligatory in forensic research. Here, we describe a voluntary collaborative exercise to test the recently developed Species Identification by Insertions/Deletions (SPInDel) method. The SPInDel kit allows the identification of species by the generation of numeric profiles combining the lengths of six mitochondrial ribosomal RNA (rRNA) gene regions amplified in a single reaction followed by capillary electrophoresis...
March 7, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28315820/evaluating-differential-nuclear-dna-yield-rates-and-osteocyte-numbers-among-human-bone-tissue-types-a-synchrotron-radiation-micro-ct-approach
#5
Janna M Andronowski, Amy Z Mundorff, Isaac V Pratt, Jon M Davoren, David M L Cooper
Molecular human identification has conventionally focused on DNA sampling from dense, weight-bearing cortical bone tissue, typically from femora or tibiae. A comparison of skeletal elements from three contemporary individuals demonstrated that elements with high quantities of cancellous bone yielded nuclear DNA at the highest rates, suggesting that preferentially sampling cortical bone may be suboptimal (Mundorff & Davoren, 2014). Despite these findings, the reason for the differential DNA yields between cortical and cancellous bone tissues remains unknown...
March 6, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28315050/forensic-use-of-y-chromosome-dna-a-general-overview
#6
REVIEW
Manfred Kayser
The male-specific part of the human Y chromosome is widely used in forensic DNA analysis, particularly in cases where standard autosomal DNA profiling is not informative. A Y-chromosomal gene fragment is applied for inferring the biological sex of a crime scene trace donor. Haplotypes composed of Y-chromosomal short tandem repeat polymorphisms (Y-STRs) are used to characterise paternal lineages of unknown male trace donors, especially suitable when males and females have contributed to the same trace, such as in sexual assault cases...
March 17, 2017: Human Genetics
https://www.readbyqxmd.com/read/28314239/likelihood-ratio-and-posterior-odds-in-forensic-genetics-two-sides-of-the-same-coin
#7
Amke Caliebe, Susan Walsh, Fan Liu, Manfred Kayser, Michael Krawczak
It has become widely accepted in forensics that, owing to a lack of sensible priors, the evidential value of matching DNA profiles in trace donor identification or kinship analysis is most sensibly communicated in the form of a likelihood ratio (LR). This restraint does not abate the fact that the posterior odds (PO) would be the preferred basis for returning a verdict. A completely different situation holds for Forensic DNA Phenotyping (FDP), which is aimed at predicting externally visible characteristics (EVCs) of a trace donor from DNA left behind at the crime scene...
March 6, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28303414/identification-of-muscidae-diptera-of-medico-legal-importance-by-means-of-wing-measurements
#8
Andrzej Grzywacz, Jakub Ogiela, Adam Tofilski
Cadavers attract numerous species and genera of Muscidae, both regular elements of carrion insect assemblages, and accidental visitors. Identification of adult Muscidae may be considered difficult, particularly by non-experts. Since species identification is a vital first step in the analysis of entomological material in any forensic entomology orientated experiment and real cases, various alternative methods of species identification have been proposed. We investigated possibility of semiautomated identification by means of wing measurements as an alternative for classic morphology and DNA-based approaches...
March 16, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28295603/rapid-abo-genotyping-by-high-speed-droplet-allele-specific-pcr-using-crude-samples
#9
Chiaki Taira, Kazuyuki Matsuda, Naoya Takeichi, Satomi Furukawa, Mitsutoshi Sugano, Takeshi Uehara, Nobuo Okumura, Takayuki Honda
BACKGROUND: ABO genotyping has common tools for personal identification of forensic and transplantation field. We developed a new method based on a droplet allele-specific PCR (droplet-AS-PCR) that enabled rapid PCR amplification. We attempted rapid ABO genotyping using crude DNA isolated from dried blood and buccal cells. METHODS: We designed allele-specific primers for three SNPs (at nucleotides 261, 526, and 803) in exons 6 and 7 of the ABO gene. We pretreated dried blood and buccal cells with proteinase K, and obtained crude DNAs without DNA purification...
March 13, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28279935/evaluation-of-the-illumina-forenseq%C3%A2-dna-signature-prep-kit-mps-forensic-application-for-the-miseq-fgx%C3%A2-benchtop-sequencer
#10
Catarina Xavier, Walther Parson
Massively Parallel (Next Generation) Sequencing (MPS) technologies have recently been proven useful and successful in typing various markers relevant in forensic genetics, such as STRs, SNPs and mitochondrial genomes. Early studies investigated self-developed DNA libraries, commercially supplied kits are currently being made available to allow a smoother and gradual implementation of such technologies in forensic laboratories. The ForenSeq™ DNA Signature Prep Kit (Illumina, CA) is the first commercially available STR kit that can be used on the MiSeq FGx™ (Illumina, CA) benchtop high-throughput sequencer...
March 1, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28273509/the-factor-of-10-in-forensic-dna-match-probabilities
#11
Simone Gittelson, Tamyra R Moretti, Anthony J Onorato, Bruce Budowle, Bruce S Weir, John Buckleton
An update was performed of the classic experiments that led to the view that profile probability assignments are usually within a factor of 10 of each other. The data used in this study consist of 15 Identifiler loci collected from a wide range of forensic populations. Following Budowle et al. [1], the terms cognate and non-cognate are used. The cognate database is the database from which the profiles are simulated. The profile probability assignment was usually larger in the cognate database. In 44%-65% of the cases, the profile probability for 15 loci in the non-cognate database was within a factor of 10 of the profile probability in the cognate database...
February 16, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28273508/helping-to-distinguish-primary-from-secondary-transfer-events-for-trace-dna
#12
Duncan Taylor, Alex Biedermann, Lydie Samie, Ka-Man Pun, Tacha Hicks, Christophe Champod
DNA is routinely recovered in criminal investigations. The sensitivity of laboratory equipment and DNA profiling kits means that it is possible to generate DNA profiles from very small amounts of cellular material. As a consequence, it has been shown that DNA we detect may not have arisen from a direct contact with an item, but rather through one or more intermediaries. Naturally the questions arising in court, particularly when considering trace DNA, are of how DNA may have come to be on an item. While scientists cannot directly answer this question, forensic biological results can help in discriminating between alleged activities...
February 20, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28271363/yfiler-%C3%A2-plus-population-samples-and-dilution-series-stutters-analytic-thresholds-and-drop-out-probabilities
#13
Mikkel Meyer Andersen, Helle Smidt Mogensen, Poul Svante Eriksen, Niels Morling
The Yfiler (Ⓡ) Plus Amplification Kit amplifies 27 Y chromosomal small tandem repeat (STR) markers. The kit has five-fluorescent dye chemistry and the improved PCR buffer system of modern STR kits. We validated the kit for accredited investigations of crime scene samples by a thorough study of kit dynamics and performance. We determined dye-dependent analytical thresholds by receiver operating characteristics (ROC) and made a customised artefact filter that includes theoretical known artefacts by use of previously analysed population samples...
March 7, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28270824/advances-of-community-level-plant-dna-barcoding-in-china
#14
Nancai Pei, Bufeng Chen, W J Kress
DNA barcoding is a commonly used bio-technology in multiple disciplines including biology, environmental science, forensics and inspection, etc. Forest dynamic plots provide a unique opportunity to carry out large-scale, comparative, and multidisciplinary research for plant DNA barcoding. The paper concisely reviewed four previous progresses in China; specifically, species discrimination, community phylogenetic reconstruction, phylogenetic community structure exploration, and biodiversity index evaluation. Further, we demonstrated three major challenges; specifically, building the impetus to generate DNA barcodes using multiple plant DNA markers for all woody species at forest community levels, analyzing massive DNA barcoding sequence data, and promoting theoretical innovation...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28269241/label-free-detection-of-sex-determining-region-y-sry-via-capacitive-biosensor
#15
Shilpa Sivashankar, Christos Sapsanis, Sumeyra Agambayev, Ulrich Buttner, Khaled Nabil Salama
In this work, we present for the first time, the use of a simple fractal capacitive biosensor for the quantification and detection of sex-determining region Y (SRY) genes. This section of genetic code, which is found on the Y chromosome, finds importance for study as it causes fetuses to develop characteristics of male sex-like gonads when a mutation occurs. It is also an important genetic code in men, and disorders involving the SRY gene can cause infertility and sexual malfunction that lead to a variety of gene mutational disorders...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28254385/dna-methylation-based-forensic-age-prediction-using-artificial-neural-networks-and-next-generation-sequencing
#16
Athina Vidaki, David Ballard, Anastasia Aliferi, Thomas H Miller, Leon P Barron, Denise Syndercombe Court
The ability to estimate the age of the donor from recovered biological material at a crime scene can be of substantial value in forensic investigations. Aging can be complex and is associated with various molecular modifications in cells that accumulate over a person's lifetime including epigenetic patterns. The aim of this study was to use age-specific DNA methylation patterns to generate an accurate model for the prediction of chronological age using data from whole blood. In total, 45 age-associated CpG sites were selected based on their reported age coefficients in a previous extensive study and investigated using publicly available methylation data obtained from 1156 whole blood samples (aged 2-90 years) analysed with Illumina's genome-wide methylation platforms (27K/450K)...
February 26, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28252872/powerplex%C3%A2-fusion-6c-system-evaluation-study-for-analysis-of-casework-and-database-samples
#17
Selena Cisana, Nicoletta Cerri, Alessandro Bosetti, Andrea Verzeletti, Venusia Cortellini
AIM: To report on the successful analysis of amplicons obtained with PowerPlex® Fusion 6C System, a highly robust 27-plex genotyping kit developed for human identification laboratories, on the Applied Biosystems® 3500 Genetic Analyzer. METHOD: We performed characterization and evaluation studies following the Scientific Working Group on DNA Analysis Methods (SWGDAM) validation guidelines, examining several critical areas of kit performance. We report the results of sensitivity, robustness, heterozygous peak height ratio, precision, concordance, caseworks, and mixture interpretations...
February 28, 2017: Croatian Medical Journal
https://www.readbyqxmd.com/read/28249201/genome-wide-screening-for-highly-discriminative-snps-for-personal-identification-and-their-assessment-in-world-populations
#18
Liming Li, Yi Wang, Shuping Yang, Mingying Xia, Yajun Yang, Jiucun Wang, Daru Lu, Xingwei Pan, Teng Ma, Pei Jiang, Ge Yu, Ziqin Zhao, Yuan Ping, Huaigu Zhou, Xueying Zhao, Hui Sun, Bing Liu, Dongtao Jia, Chengtao Li, Rile Hu, Hongzhou Lu, Xiaoyang Liu, Wenqing Chen, Qin Mi, Fuzhong Xue, Yongdong Su, Li Jin, Shilin Li
The applications of DNA profiling aim to identify perpetrators, missing family members and disaster victims in forensic investigations. Single nucleotide polymorphisms (SNPs) based forensic applications are emerging rapidly with a potential to replace short tandem repeats (STRs) based panels which are now being used widely, and there is a need for a well-designed SNP panel to meet such challenge for this transition. Here we present a panel of 175 SNP markers (referred to as Fudan ID Panel or FID), selected from ∼3...
February 16, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28244283/entire-mitochondrial-dna-sequencing-on-massively-parallel-sequencing-for-the-korean-population
#19
Sohyung Park, Sohee Cho, Hee Jin Seo, Ji Hyun Lee, Moon Young Kim, Soong Deok Lee
Mitochondrial DNA (mtDNA) genome analysis has been a potent tool in forensic practice as well as in the understanding of human phylogeny in the maternal lineage. The traditional mtDNA analysis is focused on the control region, but the introduction of massive parallel sequencing (MPS) has made the typing of the entire mtDNA genome (mtGenome) more accessible for routine analysis. The complete mtDNA information can provide large amounts of novel genetic data for diverse populations as well as improved discrimination power for identification...
April 2017: Journal of Korean Medical Science
https://www.readbyqxmd.com/read/28243771/analysis-of-four-novel-x-chromosomal-short-tandem-repeats-within-71%C3%A2-kb-of-the-xp22-3-region
#20
Takeki Nishi, Kenji Fukui, Kimiharu Iwadate
DNA testing using X-chromosomal short tandem repeat (X-STR) polymorphisms has been used in maternity/paternity and complex kinship cases. Analyses of repeat sequences, surveys on racial statistics, and development of practical applications for DNA testing continue to be reported. In this study, we identified four novel tetranucleotide STR loci located in the X chromosome, which is the basis of X-STR research. These four tetranucleotide STRs were located within 71 kb of the chromosome Xp22.3 region. Using sequence analysis of the structure of repeat sequences, we identified simple repeat sequences of TAAA, CTTT, TATC, and GATA with rare insertions...
February 27, 2017: International Journal of Legal Medicine
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